Contacts of the helix formed by residues 10 - 25 (chain A) in PDB entry 1D8K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ALA 6.2 2.0 - - - -
4A GLY* 3.9 30.1 - - - +
5A SER* 4.9 5.8 - - - +
8A TYR* 5.9 3.6 - + - -
9A LYS* 1.3 98.0 - - + +
11A GLY* 1.3 53.7 + - - +
13A LEU* 3.3 8.4 + - + +
14A ALA* 2.8 36.9 + - - +
53A TRP* 4.8 4.7 - + - -
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Residues in contact with GLY 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER 5.3 2.8 + - - -
6A SER 4.9 2.2 - - - -
7A GLY* 3.8 23.2 - - - -
9A LYS 3.4 0.8 - - - -
10A PHE* 1.3 76.7 - - - +
12A VAL* 1.3 62.6 + - - +
14A ALA* 3.2 7.3 + - - +
15A LYS* 2.9 25.3 + - - +
43A HIS* 6.0 0.2 - - - -
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY 4.0 17.6 + - - +
9A LYS 3.4 8.8 + - - +
10A PHE 3.3 0.2 - - - -
11A GLY* 1.3 77.3 - - - +
13A LEU* 1.3 64.1 + - - +
15A LYS* 3.3 2.4 + - - +
16A ILE* 3.0 45.2 + - + +
43A HIS* 3.7 31.1 + - + +
46A ILE* 4.6 10.1 - - + -
50A GLN* 4.1 21.8 - - + +
53A TRP* 5.2 1.1 - - + -
54A LEU* 4.1 15.0 - - + -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS 3.0 17.7 + - - +
10A PHE* 3.6 7.0 - - + +
12A VAL* 1.3 77.5 - - - +
14A ALA* 1.3 57.5 + - - +
16A ILE* 3.2 8.5 + - + +
17A VAL* 2.8 44.0 + - + +
53A TRP* 3.7 24.5 - - + -
54A LEU* 4.0 7.0 - - + -
58A ALA* 3.7 27.6 - - + -
59A LEU* 4.3 12.1 - - + -
62A ASN* 4.3 15.3 - - - +
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE 2.8 21.6 + - - +
11A GLY* 3.5 7.2 - - - +
13A LEU* 1.3 74.5 - - - +
15A LYS* 1.3 57.0 + - - +
17A VAL* 3.4 6.7 + - - +
18A ASN* 2.9 30.5 + - - +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLY 2.9 16.5 + - - +
14A ALA* 1.3 76.7 - - - +
16A ILE* 1.3 57.4 - - - +
18A ASN* 3.4 6.4 + - + +
19A TYR* 2.8 30.4 + - + +
40A GLU 5.0 2.8 + - - -
41A THR* 3.3 30.3 - - + +
42A GLN* 5.2 3.1 - - - +
43A HIS* 3.7 26.7 - - + +
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.0 29.9 + - + +
13A LEU* 3.5 7.2 - - + +
15A LYS* 1.3 73.9 - - - +
17A VAL* 1.3 60.8 + - + +
19A TYR* 3.3 1.7 + - - +
20A MET* 2.8 42.1 + - + +
34A LEU* 6.2 0.4 - - + -
37A ILE* 3.6 26.0 - - + -
38A LEU* 4.9 5.8 - - + -
41A THR* 3.8 22.0 - - + +
43A HIS* 4.0 6.7 - - + -
54A LEU* 3.6 36.3 - - + -
59A LEU* 4.3 25.1 - - + -
65A ILE* 5.5 0.4 - - + -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 2.8 31.2 + - + +
14A ALA* 3.7 7.0 - - - +
16A ILE* 1.3 74.1 - - + +
18A ASN* 1.3 60.7 + - - +
20A MET* 3.8 5.0 - - - +
21A LYS* 2.9 32.9 + - + +
62A ASN* 3.9 32.5 - - - +
64A LYS* 4.2 26.7 - - + -
65A ILE* 4.8 12.6 - - + -
74A PHE* 4.2 4.0 - - + -
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Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA 2.9 18.6 + - - +
15A LYS* 3.6 8.1 - - + +
17A VAL* 1.3 78.5 - - - +
19A TYR* 1.3 63.6 + - - +
21A LYS* 3.2 24.1 + - - +
22A THR* 2.8 37.5 + - - -
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Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 2.8 23.1 + - + +
16A ILE 3.6 0.9 - - - +
18A ASN* 1.3 77.0 + - - +
20A MET* 1.3 89.7 + - + +
22A THR* 3.3 4.6 + - - -
23A ARG* 2.8 58.5 + - + +
26A ARG* 6.2 1.1 - - - -
32A LEU* 3.1 12.9 - - + +
36A GLU 4.5 0.5 + - - -
37A ILE* 4.1 19.7 - - + -
40A GLU* 2.6 50.9 + - + -
41A THR* 3.6 25.1 - - + -
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 2.8 34.6 + - + +
17A VAL* 3.8 5.4 - - - +
19A TYR* 1.3 97.5 - - + +
21A LYS* 1.3 57.1 + - - +
23A ARG* 3.8 5.1 - - - +
24A HIS* 2.9 32.6 + - - +
28A ASP 5.3 0.2 - - - +
30A HIS 5.0 5.2 - - - +
32A LEU* 4.7 10.1 - - + +
37A ILE* 3.8 18.2 - - + -
65A ILE* 4.9 9.4 - - + -
72A TYR 3.3 26.9 - - - +
73A ALA* 3.7 22.2 - - - +
74A PHE* 3.8 17.2 - - + +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 2.9 21.3 + - + +
18A ASN* 3.4 25.7 + - - +
20A MET* 1.3 74.4 - - - +
22A THR* 1.3 71.8 + - - +
24A HIS* 2.9 5.7 + - - +
25A GLN* 2.7 50.6 + - + +
64A LYS* 5.1 7.6 - - - +
74A PHE* 3.3 35.8 - - + -
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN* 2.8 27.5 + - - -
19A TYR* 3.8 5.2 - - - -
21A LYS* 1.3 85.8 + - - +
23A ARG* 1.3 56.7 + - - +
25A GLN* 3.2 17.5 + - - +
26A ARG* 2.9 45.5 + - + +
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 2.8 48.0 + - + +
20A MET* 3.8 6.5 - - - +
22A THR* 1.3 71.4 - - - +
24A HIS* 1.3 62.2 + - - +
26A ARG* 3.1 24.5 + - + +
27A GLY 3.1 18.5 + - - -
28A ASP* 2.7 53.3 + - + +
30A HIS* 3.9 12.0 + - - -
32A LEU* 3.5 17.8 - - - +
40A GLU* 2.7 38.3 + - - -
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Residues in contact with HIS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET 2.9 19.6 + - - +
21A LYS 3.4 2.9 - - - +
23A ARG* 1.3 76.8 - - - +
25A GLN* 1.3 64.4 + - + +
26A ARG 3.6 0.2 + - - -
27A GLY* 3.6 3.8 + - - -
28A ASP 3.5 13.0 + - - +
29A THR* 3.2 57.0 + - + +
74A PHE* 3.2 54.1 + + + +
76A PRO* 3.8 26.9 - - + +
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 2.7 30.3 + - + +
22A THR* 3.3 20.9 - - - +
24A HIS* 1.3 75.7 - - - +
26A ARG* 1.3 66.0 + - + +
27A GLY* 4.6 0.3 - - - -
80A VAL* 5.1 16.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il